<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_orderCells" name="Monocle3 orderCells" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>along trajectories</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
LANG=en_US.UTF-8 monocle3 orderCells
    --reduction-method '${reduction_method}'
#if $root_pr_nodes
    --root-pr-nodes '${root_pr_nodes}'
#end if
#if $root_cells
    --root-cells '${root_cells}'
#end if
#if $cell_phenotype
    --cell-phenotype '${cell_phenotype}'
#end if
#if $root_type
    --root-type '${root_type}'
#end if

    @INPUT_OPTS@
    @OUTPUT_OPTS@

    @VERBOSE@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="root_pr_nodes" argument="--root-pr-nodes" type="text" optional="true" label="The starting principal points. We learn a principal graph that passes through the middle of the data points and use it to represent the developmental process. Exclusive with the root cell option."/>
    <param name="root_cells" argument="--root-cells" type="text" optional="true" label="The starting cells. Each cell corresponds to a principal point and multiple cells can correspond to the same principal point. Exclusive with the root node option."/>
    <param name="cell_phenotype" argument="--cell-phenotype" type="text" optional="true" label="The cell phenotype (column in pdata) used to identify root principal nodes."/>
    <param name="root_type" argument="--root-type" type="text" optional="true" label="The value in the cell phenotype column used to extract root nodes."/>
    <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction that was used for clustering.">
      <option selected="true" value="UMAP">UMAP</option>
      <option value="tSNE">tSNE</option>
      <option value="PCA">PCA</option>
      <option value="LSI">LSI</option>
    </param>
    <expand macro="verbose_flag"/>
  </inputs>

  <outputs>
    <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
  </outputs>

  <tests>
    <test>
      <param name="input_object_file" value="input.RDS"/>
      <param name="input_object_format" value="cds3"/>
      <param name="reduction_method" value="UMAP"/>
      <param name="cell_phenotype" value="embryo.time.bin"/>
      <param name="root_type" value="130-170"/>
      <param name="output_object_format" value="cds3"/>
      <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
==========================================
Monocle3 ordering of cells (`order_cells`)
==========================================

Order cells using the inferred graph

@HELP@

@VERSION_HISTORY@
]]></help>
  <expand macro="citations"/>
</tool>